def add_variant(variant, db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[hotspot_name]
final_qc_inc = 0
cov_qc_inc = 0
af_qc_inc = 0
multi_allele_inc = 0
if variant['FINAL_QC'] == 'PASS':
final_qc_inc = 1
if variant['COV_QC'] == 'PASS':
cov_qc_inc = 1
if variant['AF_QC'] == 'PASS':
af_qc_inc = 1
if variant['MULTI_ALLELE_QC'] == 'PASS':
multi_allele_inc = 1
wt_inc = 0
het_alt_inc = 0
het_inc = 0
hom_inc = 0
nocall_inc = 0
zygos = genotypetools.get_zygosity(variant['GT_calc'])
if 'NOCALL' in variant['FILTER']:
nocall_inc = 1
elif zygos == 'wt':
wt_inc = 1
elif zygos == 'het_alt':
het_alt_inc = 1
elif zygos == 'het':
het_inc = 1
elif zygos == 'hom':
hom_inc = 1
elif zygos == 'nocall':
nocall_inc = 1
entry = {'CHROM': variant['CHROM'], 'POS': variant['POS'], 'REF': variant['REF'], 'ALT': variant['ALT']}
variants_coll.update_one(entry, {'$inc': {'orig_stats.qc.total_count': 1,
'orig_stats.qc.final_qc_count': final_qc_inc,
'orig_stats.qc.cov_qc_count': cov_qc_inc,
'orig_stats.qc.af_qc_count': af_qc_inc,
'orig_stats.qc.multi_allele_qc_count': multi_allele_inc,
'orig_stats.zygosity.wt_count': wt_inc,
'orig_stats.zygosity.het_count': het_inc,
'orig_stats.zygosity.het_alt_count': het_alt_inc,
'orig_stats.zygosity.hom_count': hom_inc,
'orig_stats.zygosity.nocall_count': nocall_inc},
'$addToSet': {'orig_samples': variant['SAMPLE']}},
upsert=True)
if db is None:
client.close()
def add_new_sample(new_sample, db=None):
if db is None:
client, db = mongo.get_connection()
sampleinfo_coll = db['sample_info']
sampleinfo_coll.update_one(new_sample, {'$set': new_sample}, upsert=True)
if db is None:
client.close()
def delete_sample(sample, db=None):
if db is None:
client, db = mongo.get_connection()
sampleinfo_coll = db['sample_info']
sampleinfo_coll.remove_one({"project_name": project_name, "SAMPLE": sample})
if db is None:
client.close()
def get_sample_vars(sample, type, db=None):
global variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
sample_vars = variants_coll.find({'TYPE': type, 'SAMPLE': sample})
return sample_vars
def count_samples(db=None):
global variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
sample_vars = variants_coll.distinct('SAMPLE')
return len(sample_vars)
def add_variant(variant, db=None):
global variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
variants_coll.insert(variant)
if db is None:
client.close()
def drop_variants_index(db=None):
global project_name, variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
variants_coll.drop_indexes()
if db is None:
client.close()
def get_collection(db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
if db is None:
client.close()
return hotspot_coll
def get_collection(db=None):
global variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
if db is None:
client.close()
return variants_coll
def add_new_hist(number, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
new_hist = {"PROJECT": project_name, "NUMBER": number}
hotspothist_coll = db['hotspot_history']
hotspothist_coll.update_one(new_hist, {'$set': new_hist}, upsert=True)
if db is None:
client.close()
def change_config_field(field, value, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
config_coll = db['configs']
config_coll.update_one({'project_name': project_name}, {'$set': {field: value}})
if db is None:
client.close()
def create_project_config(config, db=None):
if db is None:
client, db = mongo.get_connection()
configs_coll = db['configs']
configs_coll.replace_one(config, config, upsert=True)
if db is None:
client.close()
return config
def change_sample_field(sample, field, value, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
sample_info_coll = db['sample_info']
sample_info_coll.update_one({'PROJECT': project_name, 'SAMPLE': sample}, {'$set': {field: value}})
if db is None:
client.close()
def get_affected(sample_name, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
sample_info_coll = db['sample_info']
info_doc = sample_info_coll.find_one({"project_name": project_name, "SAMPLE": sample_name})
if db is None:
client.close()
return info_doc['AFFECTED']
def index_hotspot(db=None):
global project_name, hotspot_name
index = [("CHROM", ASCENDING), ("POS", ASCENDING)]
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
hotspot_coll.create_index(index)
if db is None:
client.close()
def get_next_number(db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
hotspothist_coll = db['hotspot_history']
total_count = hotspothist_coll.find({"PROJECT": project_name}).count()
if db is None:
client.close()
return total_count + 1
def get_variant(chrom, pos, ref, alt, db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
hotspot = hotspot_coll.find_one({"CHROM": chrom, "POS": pos, "REF": ref, "ALT": alt})
if db is None:
client.close()
return hotspot
def index_variants(db=None):
global project_name, variants_name
index = [("TYPE", ASCENDING), ("CHROM", ASCENDING), ("POS", ASCENDING)]
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
variants_coll.create_index(index)
if db is None:
client.close()
def is_fully_annotated(sample, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
proj_collection = db['sample_info']
result = proj_collection.find_one({"PROJECT": project_name, "SAMPLE": sample})
if "FULLY_ANNOTATED" in result.keys() and result['FULLY_ANNOTATED'] is True:
return True
else:
return False
def is_sample(sample, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
proj_collection = db['sample_info']
result = proj_collection.find_one({"PROJECT": project_name, "SAMPLE": sample})
if result is not None:
return True
else:
return False
def get_project_config(db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
configs_coll = db['configs']
project_config = configs_coll.find_one({'project_name': project_name})
if db is None:
client.close()
return project_config
def get_samples(db=None):
if db is None:
client, db = mongo.get_connection()
sample_info = get_sample_info(db)
samples = []
for id in sample_info:
samples.append(id)
if db is None:
client.close()
return samples
def get_hotspot_vars(db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
sortby = [('CHROM', ASCENDING), ('POS', ASCENDING)]
hotspot_cursor = hotspot_coll.find().sort(sortby)
if db is None:
client.close()
return hotspot_cursor
def has_loaded_hotspots(number, db=None):
global project_name, variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
var_match = variants_coll.find_one({"PROJECT": project_name, "TYPE": "hotspot", "NUMBER": number})
if db is None:
client.close()
if var_match is None:
return False
else:
return True
def is_hotspot_hist(number, db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
hotspothist_coll = db['hotspot_history']
hotspot_hist = hotspothist_coll.find_one({"PROJECT": project_name, "NUMBER": number})
if db is None:
client.close()
if hotspot_hist is None:
return False
else:
return True
def save_annotation(chrom, pos, ref, alt, annotations, db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
search = {'CHROM': chrom, 'POS': pos, 'REF': ref, 'ALT': alt}
update = {'$set': {'ANNOTATION': annotations}}
matched_count = hotspot_coll.update_one(search, update).matched_count
if matched_count != 1:
print 'Variant not found in hotspot'
if db is None:
client.close()
def is_sample_loaded(sample, type, db=None):
global variants_name
if db is None:
client, db = mongo.get_connection()
variants_coll = db[variants_name]
sample_var = variants_coll.find_one({'TYPE': type, 'SAMPLE': sample})
if db is None:
client.close()
if sample_var is not None:
return True
else:
return False
def has_annotation(chrom, pos, ref, alt, db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
hotspot_coll = db[hotspot_name]
hotspot = hotspot_coll.find_one({"CHROM": chrom, "POS": pos, "REF": ref, "ALT": alt})
if db is None:
client.close()
if 'ANNOTATION' in hotspot.keys():
return True
else:
return False
def is_hotspot(chrom, pos, ref, alt, db=None):
global hotspot_name
if db is None:
client, db = mongo.get_connection()
query = {'CHROM': chrom, 'POS': pos, 'REF': ref, 'ALT': alt}
hotspot_coll = db[hotspot_name]
match = hotspot_coll.find_one(query)
if db is None:
client.close()
if match:
return True
else:
return False
def has_sample_info(db=None):
global project_name
if db is None:
client, db = mongo.get_connection()
sample_info_coll = db['sample_info']
info_doc = sample_info_coll.find_one({"PROJECT": project_name})
if db is None:
client.close()
if info_doc is not None:
return True
else:
return False